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Cadmium in PDB 6enw: X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin, PDB code: 6enw was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.43 / 2.60
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.878, 180.878, 180.878, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.6

Other elements in 6enw:

The structure of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Gold (Au) 2 atoms
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin (pdb code 6enw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin, PDB code: 6enw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 6enw

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Cadmium binding site 1 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:27.1
occ:0.40
 OE2 A:GLU11 2.4 24.9 1.0
OE1 A:GLU11 2.5 26.0 1.0
CD A:GLU11 2.8 23.3 1.0
O A:HOH415 3.0 13.1 1.0
OG1 A:THR10 3.9 23.7 1.0
CG A:GLU11 4.4 21.6 1.0
NE2 A:GLN120 4.4 27.4 1.0
OE1 A:GLN120 4.7 29.8 1.0
CB A:SER9 4.7 15.5 1.0
N A:THR10 4.9 17.4 1.0
CD A:GLN120 5.0 27.2 1.0

Cadmium binding site 2 out of 10 in 6enw

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Cadmium binding site 2 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:50.1
occ:0.40
 O A:HOH355 2.1 2.0 0.4
OE2 A:GLU53 2.5 23.4 0.4
O A:HOH393 2.5 5.1 0.4
OE2 A:GLU56 2.7 60.6 1.0
OE2 A:GLU53 2.8 29.7 0.6
OE1 A:GLU53 2.8 24.4 0.4
CD A:GLU53 3.0 23.4 0.4
CD A:GLU53 3.5 28.5 0.6
CD A:GLU56 3.7 49.6 1.0
OE1 A:GLU53 3.9 28.5 0.6
O A:HOH375 3.9 43.8 1.0
OE1 A:GLU56 4.2 50.4 1.0
CG A:GLU53 4.4 23.3 0.4
CG A:GLU53 4.6 27.2 0.6
CB A:GLU53 4.7 25.6 0.6
CG A:GLU56 4.9 41.2 1.0
CB A:GLU53 5.0 23.2 0.4

Cadmium binding site 3 out of 10 in 6enw

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Cadmium binding site 3 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:49.4
occ:0.40
 OE1 A:GLU56 2.4 50.4 1.0
OE1 A:GLU60 2.5 56.5 1.0
O A:HOH344 2.6 5.5 0.4
OE2 A:GLU60 3.1 53.2 1.0
CD A:GLU60 3.2 47.7 1.0
CD A:GLU56 3.6 49.6 1.0
OE1 A:GLU53 3.8 28.5 0.6
OE2 A:GLU56 4.4 60.6 1.0
CG A:GLU57 4.5 40.3 1.0
O A:HOH421 4.6 22.1 1.0
CG A:GLU56 4.6 41.2 1.0
CG A:GLU60 4.6 39.8 1.0
O A:HOH393 4.8 5.1 0.4
CD A:GLU53 4.9 28.5 0.6

Cadmium binding site 4 out of 10 in 6enw

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Cadmium binding site 4 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:20.8
occ:0.50
 OD2 A:ASP80 3.0 13.2 1.0
OD1 A:ASP80 3.5 15.0 1.0
CG A:ASP80 3.7 15.8 1.0
O A:HOH341 4.2 38.0 1.0

Cadmium binding site 5 out of 10 in 6enw

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Cadmium binding site 5 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:34.5
occ:0.40
 O A:HOH304 1.8 10.9 0.4
NE2 A:HIS132 2.6 50.8 1.0
CE1 A:HIS132 3.5 50.1 1.0
CD2 A:HIS132 3.6 45.9 1.0
O A:HOH408 4.3 32.6 1.0
ND1 A:HIS132 4.7 46.6 1.0
CD A:CD209 4.7 41.1 0.3
CG A:HIS132 4.7 42.1 1.0

Cadmium binding site 6 out of 10 in 6enw

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Cadmium binding site 6 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:31.5
occ:0.30
 OE1 A:GLU130 2.2 44.7 1.0
CD A:GLU130 3.0 42.7 1.0
OE2 A:GLU130 3.1 57.0 1.0
CL A:CL211 3.3 2.1 0.4
CG A:GLU130 4.5 36.8 1.0
CD A:CD210 4.9 75.5 0.3

Cadmium binding site 7 out of 10 in 6enw

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Cadmium binding site 7 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:70.3
occ:1.00
 SG A:CYS48 2.4 22.5 1.0
CE1 A:HIS49 3.1 50.9 0.5
CB A:CYS48 3.2 19.8 1.0
ND1 A:HIS49 3.3 46.2 0.5
O A:HOH399 3.4 21.1 1.0
NE2 A:HIS49 3.5 55.0 0.5
ND1 A:HIS49 3.6 46.2 0.5
NH1 A:ARG52 3.7 39.0 1.0
CG A:HIS49 3.7 42.6 0.5
N A:HIS49 3.8 23.3 0.5
N A:HIS49 3.8 23.3 0.5
CD2 A:HIS49 3.9 46.6 0.5
C A:CYS48 3.9 20.7 1.0
CD A:ARG52 4.0 33.1 1.0
CA A:CYS48 4.2 19.6 1.0
O A:GLU45 4.2 17.3 1.0
CE1 A:HIS49 4.3 50.9 0.5
CA A:HIS49 4.3 26.6 0.5
CA A:HIS49 4.3 26.6 0.5
O A:CYS48 4.4 18.5 1.0
CG A:HIS49 4.4 42.6 0.5
CZ A:ARG52 4.6 40.0 1.0
CB A:HIS49 4.6 31.8 0.5
CB A:HIS49 4.6 31.8 0.5
NE A:ARG52 4.8 35.9 1.0
O A:HOH383 4.9 15.6 1.0
CG A:GLU45 4.9 37.0 1.0

Cadmium binding site 8 out of 10 in 6enw

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Cadmium binding site 8 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:51.4
occ:0.30
 O A:HOH403 2.4 45.8 1.0
OE1 A:GLU45 2.7 47.0 1.0
O A:HOH328 3.0 16.4 1.0
O A:HOH409 3.5 32.7 1.0
CD A:GLU45 3.6 46.2 1.0
OE2 A:GLU45 3.9 54.8 1.0
O A:HIS173 4.0 0.8 1.0
ND1 A:HIS173 4.5 0.6 1.0
NH1 A:ARG168 4.6 17.8 1.0
CB A:HIS173 4.7 0.7 1.0
CG A:GLU45 4.8 37.0 1.0
NH2 A:ARG168 4.9 16.9 1.0
CG A:HIS173 4.9 0.8 1.0
C A:HIS173 5.0 0.2 1.0

Cadmium binding site 9 out of 10 in 6enw

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Cadmium binding site 9 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:41.1
occ:0.30
 OD2 A:ASP127 2.4 42.3 1.0
CG A:ASP127 3.1 39.2 1.0
OD1 A:ASP127 3.1 37.2 1.0
OG A:SER131 3.5 41.9 1.0
CB A:SER131 4.3 38.0 1.0
CB A:ASP127 4.6 34.9 1.0
CD A:CD205 4.7 34.5 0.4
O A:ASP127 4.8 26.4 1.0

Cadmium binding site 10 out of 10 in 6enw

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Cadmium binding site 10 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:75.5
occ:0.33
 OD1 A:ASP127 3.7 37.2 1.0
OG A:SER131 4.1 41.9 1.0
OE1 A:GLU130 4.4 44.7 1.0
O A:HOH459 4.6 30.3 0.3
CG A:ASP127 4.9 39.2 1.0
CD A:CD206 4.9 31.5 0.3

Reference:

D.M.Monti, G.Ferraro, G.Petruk, L.Maiore, F.Pane, A.Amoresano, M.A.Cinellu, A.Merlino. Ferritin Nanocages Loaded with Gold Ions Induce Oxidative Stress and Apoptosis in Mcf-7 Human Breast Cancer Cells. Dalton Trans V. 46 15354 2017.
ISSN: ESSN 1477-9234
PubMed: 29072740
DOI: 10.1039/C7DT02370G
Page generated: Fri Jul 19 19:12:32 2024

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